AEFW is a problem and you need to make sure that your tank is rid of them. However, they usually do not kill the coral all the way without help from other environmental things.
Slow death from the bottom up is usually a parameter or two being too far out of whack for too long, or poor lighting that is causing too many shadows. Have you gone back to the basics and recalibrated your refractometer, checked your temp using something with mercury, checked your test kits, etc.?
They could also just be suffering from all of the dipping and handling. Not much you can do about this.